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Crystal structure of human DHODH with OSU-03012
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 Ammonium sulfate, glycerol, DHO, DDAO, OSU-03012
Crystal Properties Matthews coefficient Solvent content 3.72 66.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.006 α = 90 b = 91.006 β = 90 c = 123.069 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2018-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.999873 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 50 99 0.07 0.999 19.21 9.53 114363
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 94.2 0.545 0.878 2.76 6.52
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OQV 1.4 48.55 107176 5622 97.66 0.1524 0.15078 0.1506 0.18409 0.1867 RANDOM 22.869
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.69 -0.35 -0.69 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.741 r_dihedral_angle_4_deg 20.111 r_dihedral_angle_3_deg 12.702 r_rigid_bond_restr 11.419 r_long_range_B_refined 8.137 r_long_range_B_other 8.102 r_scangle_other 7.984 r_mcangle_it 6.808 r_mcangle_other 6.806 r_scbond_it 6.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.741 r_dihedral_angle_4_deg 20.111 r_dihedral_angle_3_deg 12.702 r_rigid_bond_restr 11.419 r_long_range_B_refined 8.137 r_long_range_B_other 8.102 r_scangle_other 7.984 r_mcangle_it 6.808 r_mcangle_other 6.806 r_scbond_it 6.8 r_scbond_other 6.798 r_dihedral_angle_1_deg 6.617 r_mcbond_it 5.75 r_mcbond_other 5.749 r_angle_refined_deg 1.711 r_angle_other_deg 1.7 r_chiral_restr 0.083 r_bond_other_d 0.018 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2785 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing XDS data scaling